sangeranalyseR
This is the development version of sangeranalyseR; for the stable release version, see sangeranalyseR.
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Bioconductor version: Development (3.20)
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Author: Rob Lanfear <rob.lanfear at gmail.com>, Kuan-Hao Chao <ntueeb05howard at gmail.com>
Maintainer: Kuan-Hao Chao <ntueeb05howard at gmail.com>
citation("sangeranalyseR")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("sangeranalyseR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sangeranalyseR")
sangeranalyseR | HTML | R Script |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Alignment, GUI, Genetics, Preprocessing, QualityControl, SangerSeq, Sequencing, Software, Visualization |
Version | 1.15.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
License | GPL-2 |
Depends | R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger |
Imports | |
System Requirements | |
URL |
See More
Suggests | testthat (>= 2.1.0) |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | sangeranalyseR_1.15.0.tar.gz |
Windows Binary | sangeranalyseR_1.15.0.zip (64-bit only) |
macOS Binary (x86_64) | sangeranalyseR_1.15.0.tgz |
macOS Binary (arm64) | sangeranalyseR_1.15.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/sangeranalyseR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sangeranalyseR |
Bioc Package Browser | https://code.bioconductor.org/browse/sangeranalyseR/ |
Package Short Url | https://bioconductor.org/packages/sangeranalyseR/ |
Package Downloads Report | Download Stats |